Method and system for personal information extraction and modeling with fully generalized extraction contexts

ABSTRACT

Systems and methods for modeling information from a set of documents are disclosed. A tool allows a user to model concepts of interest and extract information from a set of documents in an editable format. The extracted information includes a list of instances of a document from the set of documents that contains the selected concept. The user may modify the extracted information to create subsets of information, add new concepts to the model, and share the model with others.

RELATED APPLICATIONS

This application claims the benefit of the filing date of U.S.Provisional Application No. 60/855,112, filed Oct. 30, 2006, titled“Method and System for Personal Information Extraction and Modeling,” ofVictor J. Pollara, incorporated in its entirety herein by reference.

FIELD

The present invention relates generally to information extraction, andmore particularly, to methods and systems for extracting informationfrom a collection of documents and modeling the extracted informationusing customized tools.

BACKGROUND

Today, there exists a rising flood of data and a drought of actionableinformation. People are experiencing information overload from theInternet, search engines, digital libraries (e.g., PubMed™), enterprisedatabases (e.g., electronic case files), and even personal desktops.There exists the need for a tool that may organize, aggregate, model,and analyze information, as well as provide ways for people to use theknowledge gained. For example, many researchers need to share, leverage,retain, and re-use information retrieved from a search. Accordingly,there exists the need for a personal information extraction and modeling(“PIEM”) tool that may transform a labor intensive, manual, many-timeprocess into an efficient, flexible process.

SUMMARY

A piece of text may have different meanings, depending on the context inwhich it is found. For example, when a sports announcer discusses a“lowball,” he is probably talking about something different than a realestate agent discussing a “lowball.” Also, within a single document,meaning and possible relevance of a concept may be different indifferent sections of the document.

There exists the need for a tool for extracting and interpretingconcepts differently on the basis of their context in a document. Forexample, in a news article about a governor, the only thing that may berelevant to a reader is the governor's position on a cigarette tax, sothe user may only want to locate and extract those parts of the articlethat pertain to the governor's position on that tax and disregard therest. In a medical journal article, mention of Type 2 diabetes hasdiffering degrees of importance, depending on which context it appears.

Combining the power of visual modeling with information extraction, asdescribed in U.S. application Ser. No. 11/434,847, entitled “Method andSystem for Information Extraction and Modeling,” filed May 17, 2006 andincorporated herein by reference (“the '847 application”), opens theopportunity to use concept-based extraction and modeling in a way toconcisely control both the terms that are being sought, and the contextin which they are sought. PIEM technology (which may also be calledpersonal knowledge extraction and management technology, or “PKEM”technology) can provide a populist home for extraction techniques that,to date, have remained in the world of specialists and academics.Specifically, a PIEM tool may allow extraction and modeling of conceptsincluding a pattern (i.e., what the user is looking for) and/or acontext (i.e., where to look for the pattern). For example, a patternmay include: a set of terms, a group of concepts combined by arelationship, boolean or other combinations of concepts, or syntactic orlinguistic groupings. A concept may include: a set of documents, a setof sentences or other syntactically defined text blocks, a set oflinguistically defined text blocks, a set of metadata, a set of textfragments identified by an existing concept, or a set of manuallydefined text fragments.

The core concepts of the PIEM tool are so compelling that ultimatelyevery document management tool may incorporate its functionalities toenhance users' ability to read, understand, reason with, and act uponinformation in their documents. Other search tools, as they exist today,are simply not enough, and in the future, will not be the lastcomputer-aided step in a user's reading of documents.

PIEM may be embodied in stand-alone tools, as well as in extensions toexisting tools and services, such as, for example, today's searchengines (web and enterprise-based), existing knowledge managementproducts, document management tools, libraries and other on-lineservices, trade-focused databases such as PubMed™, LexisNexis™, IEEEDigital Library™, Wikipedia™, Answers.com™, and other general webinformation sources, or in enterprise libraries and data warehouses.

PIEM technology goes beyond any single specific tool, in the sense thatit creates a new class of exchangeable objects that potentially havehigh value—namely, models. Users may still enter keywords in web-basedsearch services such as Yahoo! or Google™, but using PIEM technology,they may also enter models and expect the service to return a set ofdocuments well-matched to the model. Conversely, after a search, a usermay receive not just a list of links, but also a list of suggestedmodels that match the documents (e.g., by some relevant calculation).

Web-based services may also serve as exchanges for models. Publishersmay provide not only a subscription to their journals, but also offerlibraries of curated models on the subjects covered by theirpublications. News outlets may provide sets of news articles on specifictopics, together with models that make it easy to “power-read” the setof articles. Whereas currently available technology may requireexpensive systems and trained model-building experts to build usefulmodels, PIEM opens the door to any domain expert or non-expert (such asa biologist, historian, political scientist, hobbyist, etc.) to engagein model building and sharing.

All manner of models (e.g., maps, timelines, diagrams, flowcharts,circuits, biological depictions, etc.) may be pluggable and immediatelyuseable and modifiable. PIEM technology also makes use of first classnatural language processing and part of speech tagging, and mayrecognize every common file type and special purpose file type. PIEMtechnology has intelligent n-gram analysis and concept clustering, and apluggable interface for all manner of thesauri, lexica, and otherdomain-specific resources. It may also include a rich suite ofpost-processing functionality that allows a user to easily craftdecision logic and otherwise make analytical use of information. It mayinclude a full fledged visualization capability to view results ofextractions and analyses, and may be configurable as either astand-alone tool or as a shared, server-based enterprise productivitytool (e.g., an add-on to existing knowledge management suites).

As an example, a hobbyist building a personal encyclopedic resource onhis or her subject of interest (this could also be a person with ahealth issue, who desperately wants to know everything that is knownabout the condition) may use the PIEM tool. Similarly, non-scienceauthors and scientists writing articles and books (with access toelectronic copies of their resource documents) may use the PIEM tool tocross-reference and tag source materials. Journalists may use the PIEMtool to organize news feeds relevant to a subject they are working on.Consultants or experts regularly tasked with developing white papers onspecific subjects may use it to not only explore a body of literature,but also to aggregate facts across documents and vet the reliability andutility of the information. Lawyers may use the PIEM tool for custommodeling of the content of legal, business, and technology documents.Students might use the PIEM tool for work on a large project thatrequires rapidly digesting a large body of literature and makingintelligent use of the information. As another example, investors whowant to study a particular area would want not only business news, butalso information about their product or service and the products orservices of competitors, as well as the underlying technology if theproduct embodies an emerging technology.

Methods consistent with embodiments of the invention model informationfrom a set of documents. A set of concepts and corresponding extractorsare imported, and a model including representations of the concepts iscreated. Based on a user selection of the representation of a firstconcept, information related to the first concept is extracted from theset of documents using the corresponding extractor, and the extractedinformation is displayed in a format that is editable by the user.

Methods consistent with embodiments of the invention allow forpersonalizing a model of information. A set of documents is downloaded,and a model containing concepts and corresponding extractors isreceived. Information related to the concepts is extracted from the setof documents using the corresponding extractors. Based on the extractedinformation, an additional concept for the model is defined to includeat least two of the concepts in the model occurring in a context.

Methods consistent with embodiments of the invention allow forannotating a set of documents in a model of information. A set ofdocuments is downloaded, and a model containing concepts andcorresponding extractors is received. Information related to theconcepts is extracted from the set of documents using the correspondingextractors. A definition for a function to calculate the status of adocument in the set of documents is received. After extractinginformation, a document in the set of documents is automaticallyannotated based on the definition.

Methods consistent with embodiments of the invention allow for modelinginformation from a set of documents. A set of concepts and correspondingextractors is imported, and a model including representations of theconcepts is created. Based on a user selection of a representation of afirst concept, information related to the first concept is extractedfrom the set of documents using the corresponding extractor. The time ofextraction of information is stored, and the extracted information isdisplayed in a format that is editable by the user.

Other embodiments of the invention provide a system for modelinginformation from a set of documents, comprising a importing componentconfigured to import a set of concepts and corresponding extractors; amodeling component configured to create a model includingrepresentations of the concepts; an extraction component configured toextract information, based on a user selection of a representation of afirst concept, related to the first concept from the set of documentsusing the corresponding extractor; a database configured to store thetime of extraction of information; and a display component configured todisplaying the extracted information in a format that is editable by theuser.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow diagram of an exemplary process to extract and modelinformation consistent with an embodiment of the present invention;

FIG. 2 is a diagram of components in an exemplary information extractionand modeling system consistent with an embodiment of the presentinvention;

FIG. 3 is a flow diagram of an exemplary process to create and modifymodels information consistent with an embodiment of the presentinvention; and

FIGS. 4-34 illustrate exemplary user interface displays consistent withan embodiment of the present invention.

DETAILED DESCRIPTION

The following detailed description refers to the accompanying drawings.Wherever possible, the same reference numbers are used in the drawingsand the following description to refer to the same or similar parts.While several exemplary embodiments and features of the invention aredescribed herein, modifications, adaptations and other implementationsare possible, without departing from the spirit and scope of theinvention. For example, substitutions, additions or modifications may bemade to the components illustrated in the drawings, and the exemplarymethods described herein may be modified by substituting, reordering, oradding steps to the disclosed methods. Accordingly, the followingdetailed description does not limit the invention.

FIG. 1 is a flow diagram of an exemplary process 100 that may be used toextract and model information consistent with an embodiment of thepresent invention. As shown in FIG. 1, a user may search within adocument set (step 110), for example using systems and methods describedin the '847 application. For example, a user may locate relevant textdocuments within a document set downloaded from a database such asPubMed™. Next, the user may analyze the information (step 120) tounderstand the documents. A PIEM tool consistent with embodiments of thepresent invention (as described in more detail below with respect toFIG. 2) may provide for concept-based extraction, concept modeling,automated text linking, information visualization, pruning andsub-setting, annotations, ranking, shareable models, exportabledatabases, and incremental updates, among other features. The user maycommunicate any extracted information with others (step 130), forexample by sharing a model, documents, or information extracted from thedocuments.

In one example, the Army Corps of Engineers may want to know what work acertain company has done for the Army Corps of Engineers in the past andmay ask questions of the company such as: who has experience, who areexperts in the field, etc. A manager for the company may create variousconcepts using the PIEM tool, and may extract information to answer thequestions. For example, to represent the Army Corps of Engineers, themanager may create a concept for “Army Corps of Engineers,” usingvariations of words that may represent “Army Corps of Engineers,” andmay associate the concept with various text strings, such as “Corps,”“COE,” Army COE,” etc. The PIEM tool may then return information relatedto that concept (e.g., return all occurrences of those text strings.)Similarly, the manager may create and combine concepts to represent theacademic degrees of its employees and the timing of certain projects todetermine, for example, which individuals are currently working onprojects related to the Army Corps of Engineers, and what theireducation level is. Combining concepts in this way may allow for complexconcept creation.

FIG. 2 is a diagram of components in an exemplary information extractionand modeling system 200 consistent with an embodiment of the presentinvention. As shown in FIG. 2, a personal knowledge extraction andmodeling (“PIEM”) tool 205 may include an extraction engine 220, avisualization tool 230, and a model editor 240. PIEM tool 205 may, incertain embodiments, include a graphical user interface, documentprocessing tools, and may allow for model import and export, as well asmanagement of models, concepts, analysis, results, and document sets.One skilled in the art will recognize that any combination of extractionengines 220, visualization tools 230, and/or model editors 240 may beused in PIEM tool 205, and that each component in system 200 may beseparate or combined. For example, in certain embodiments, document set210 or model 250 may be included in tool 205.

Extraction engine 220 may access a set of documents 210, for exampleusing a database. Document set 210 may include a set of text documentsfrom a user's personal desktop, paper documents that have been scannedinto electronic format, or information downloaded from the Internet orother databases, for example. One skilled in the art will recognize thatdocument set 210 may include any set of text, graphics, source code, orother information. For example, document set 210 may include audiofiles, such as recordings of conversations. Using speech recognitionsoftware, extraction software in extraction engine 220 may recognizeemotion in speech quality. The user may create concepts that are textbased, or concepts that may include audio clips. As another example,document set 210 may include music recordings, and extraction processesfor the music recordings may include clips of music, musical phrases, orparts of compositions. As yet another example, document set 210 mayinclude video files, such as MPEG files.

Extractors used in extraction engine 220 may include the features of theexamples described above (e.g., musical phrases or audio clips), as wellas features specifically designed to find the kinds of visuals used inthe “cutting room” (e.g., close-ups, people, background, speed,lighting, etc.) Additionally, extraction engine 220 may make an n-gramdetermination using document set 210, and may perform syntacticanalysis, lexical analysis, and simple statistical analysis, as well asother processes using document set 210, for example as described in moredetail in the '847 application. PIEM tool 205 may associate anextraction process with each concept.

Extraction Patterns

Aside from extractors for specialized resources (e.g., MPEG), there isno technical limitation on the sophistication of an extraction patternor process used by extraction engine 220. Extraction patterns may becreated from hidden Markov models, statistical approaches, machinelearning plug-ins, etc. As an example, the label “bread” may be used torepresent different concepts in different contexts. To formalize theconnection between concepts and extraction, a user may include thecontext he is working in. Assuming R is a set of information resources{r_(i)} (e.g. documents), and C is a context found in an informationresource (e.g. title, abstract), one may associate with concept K, theextraction process, X_(K) that is applied to each (r_(i), C) pair. Let(R:C) represent the set of (r_(i), C) pairs.

X is an algorithm that identifies the instances of K within C in eachr_(i)εR if they exist. The result of executing the process X_(K) on(R:C) is another set of “resource-context” pairs:

One of the most fundamental constructs available in set theory is theCartesian product. There are many natural and useful constructs that aredefined in terms of products. Given an ordered pair of concepts (K₁,K₂), associated with a pair of extraction processes ((R₁:C₁), X_(K1)),(R₂:C₂), X_(K2))), employing both extractors gives rise to the orderedpair ((R_(K1):C_(K1)), (R_(K2):C_(K2))).

Boolean Operations

Boolean operations may be used to create extraction patterns. What isthe concept “K₁ & K₂”? Intuitively, it means that both concepts appearin the same context. Let concepts K₁, K₂, be associated with a pair ofextraction processes ((R₁:C₁),X_(K1)), ((R₂:C₂), X_(K2)), with(R₁:C₁)=(R₂:C₂). Employing both extractors gives rise to the pair ofsets (R_(K1):C_(K1)), (R_(K2):C_(K2)). The natural set-theoreticoperation to perform is: (R_(K1):C₁)∩(R_(K2):C₁). This definition of“&”, with (R₁:C₁)=(R₂:C₂) is the same as: “collocation within scope R₁and context C₁.”

Multi-Field Extraction

There is much more one can do with Cartesian products consistent withembodiments of the present invention. As another example, multi-fieldextraction is possible. If a user looks for a concept like the word“currently” in resumes, an extractor in extraction engine 220 may searchfor specific fields: (currently)(rest of sentence). Each field isactually a concept in its own right and the extractor is looking for anordered pair of concepts. Let concepts K₁, K₂, be associated withextraction processes ((R₁:C₁), X_(K1)), ((R₂:C₂), X_(K2)) with(R₁:C₁)=(R₂:C₂). A “sequencing” constraint may be imposed. This can bewritten with a SEQ operator that extracts two concepts in sequence as:((R₁:C₁), SEQ(X_(K1), X_(K2))).

Multi-Context Extraction

As yet another example, multi-context extraction is possible usingextraction engine 220. Given a fixed set of documents, imagine theconcept: All (Author, Pubdate, Abstract) triples from documents with:Authorname below M in alphabetical order (K₁), Publication date afterDec. 31, 1999 (K₂), and Abstract containing “lipitor” (K₃). This conceptis defined across three different contexts within each document. Thatis, the component concepts: K₁, K₂, K₃, are associated with a threecomponent extraction process. ((R₁:C₁), X_(K1)), ((R₂:C₂), X_(K2)),((R₃:C₃), X_(K3)), with R₁=R₂=R₃, C₁≠C₂≠C₃. There is no sequencingconstraint; it is represented as a triple: ((R₁:(C₁, C₂, C₃)), (X_(K1),X_(K2), X_(K3))) where the extractors are applied component wise.

The Table: A Classic “Multi-Context” Information Resource

The table is an example of a classic multi-context information resource.In one example, a “scope” may be defined as the listing of specificinstances of a context, such as the row numbers in a table, and a“context” may be defined as the column definition in the table. In Table1 below, the scope is the listing of row numbers “1”, “2”, and “3”, andthe context is “Novel Titles.”

TABLE 1 Scope Novel Titles 1 Moby Dick 2 Tale of Two Cities 3 1984

A user could specify a subset to create a new concept, such as “19^(th)Century Novel Titles.” This new concept “19^(th) Century Novel Titles”includes a different “scope” than that shown in Table 1.

In other words, a table may include n rows and m columns, where each rowis an information resource r_(i). The set of rows may represent a scopeR={r_(i, i)=_(1, . . . , n)}. Each column of the table may represent aseparate context, C_(j, j=1, . . . , m). For example, (R:C₃) is thescope equal to “all rows”, and context is the third column.

How a Concept Defines a Scope and Context

If concept K₁ is associated with an extraction process ((R₁:C₁),X_(K1)), employing an extraction may give rise to the set(R_(K1):C_(K1)). By definition, (R_(K1):C_(K1)) is a “scope/context”pair. So it is possible to define a new concept K₂, associated with theprocess (R_(K1):C_(K1)), K₂). That is, K₂ is defined within the “result”of K₁. In certain embodiments, PIEM tool 205 facilitates such“drilldown.”

How a Scope and Context Defines a Concept

A set of resources R, and a context C within the resources of R, maydefine a concept using a minimal extractor necessary to identify C ineach r_(i)εR. The extractor may be trivial, or highly complex, asdescribed in the following example:

-   -   1. In a set, R, of raw text documents, with C=“whole document”,        the extractor is a set of whole documents.    -   2. In a set, R, of HTML pages, with C=“HTML title”, the        extractor retrieves the bytes between the tags <TITLE> and        </TITLE>.    -   3. R is a set of documents, and C is defined by a highly        complex, machine-learning algorithm X.    -   4. If a table with n rows and m columns is viewed as a        scope/context pair: ({r_(i i=1, . . . , n)}:C₁ x . . . x C_(m)),        then the trivial extractor turns the table into a concept.

This observation opens up enormous possibilities for intuitive,user-directed, post-extraction analysis because users may now do totables of extracted information anything they can do with a spreadsheet,and more.

As shown in FIG. 2, extraction engine 220 may communicate withvisualization tool 230. Visualization tool 230 may communicate withmodel editor 240, which in turn may communicate with extraction engine220. Model editor 240 may use explicit and implicit concept definitionsto build new concepts and edit existing concepts (e.g., using avisual-based editor and capturing user actions), to create, edit, andmodify model 250. Model 250 may include, for example, the model(s)described in the '847 application. One skilled in the art will recognizethat many means and methods may be used to create model 250. Forexample, a web page, document, graph, map, table, spreadsheet,flowchart, or histogram may be used to represent model 250.

Visualization tool 230 may allow a user to view, organize, and annotatemodels 250, concepts, original text from documents 210, resultsextracted from document set 210, etc. Visualization tool 230 may allow auser to annotate each document with personalized notes, associate thesenotes with the documents, and store the notes.

In certain embodiments, visualization tool 230 may allow users to buildreports 260 to visualize certain results. Reports 260 may includereports known in the art, such as web pages, documents, graphs, maps,tables, spreadsheets, flowcharts, histograms, etc. Further,visualization tool 230 may allow a user to define a simple function torank documents or to assign them statuses. Visualization tool 230 mayallow a user to define functions that depend on one or more fields in adatabase, and model editor 240 may allow the user to generate a newconcept using the function. PIEM tool 205 may associate an entireprocess (e.g., extraction and post extraction calculation) with a newconcept node in model 250 for later use.

FIG. 3 is a flow diagram of an exemplary process 300 that may be used tocreate and modify models of information consistent with an embodiment ofthe present invention. Medical experts and researchers often need toconsult research literature to find answers for specific questions aboutmedical conditions and their treatments. On any given topic, there maybe thousands of clinical trials that address some aspect of that topic.A common first step is to search a medical database, such as NationalLibrary of Medicine's PubMed™ or a subscription service such as Ovid™.Typically, a researcher will enter a boolean combination of terms and asearch engine will return the abstracts that match those terms. A resultof a search of MedLine™, for example, may produce over a thousandentries on the subject of treatments for diabetics. PIEM tool 205 mayparse the data produced from the search, and may extract some metadata,such as title and publication date, as well as the abstract of eachentry. After such a search has been conducted, as shown in FIG. 3, auser may download results (e.g., all documents, or various combinationsof metadata or abstracts).

As shown in FIG. 3, a user may download documents, for example in theform of document set 210 (step 310), to the user's computer, a networkdrive, a wireless device, other media, etc. The document set may resultfrom a search as described above or may be received from another user,etc. Next, the user may create a new project with document set 210 usingPIEM tool 205 (step 320). PIEM tool 205 may upload document set 210 inany format, such as XML, “.txt”, “.pdf”, “.doc”, or “.html”, forexample.

Next, the user may determine if resources (e.g., other models, concepts,and/or extractors) are available to apply to document set 210 (step330). If a user has resources available (step 330, Yes), for example ifthe user received a general model for clinical trials abstracts from acolleague, the user may import at least one concept from that model intothe current project (step 340). The user may also import any relatedextractors into the current project. PIEM tool 205, may, in certainembodiments, automatically import any extractors associated withimported concepts. The extractors may incorporate many different typesof search tools such as word frequency vectors, heuristic textsummaries, construct frequencies, entity-relations, etc., as describedin the '847 application.

If the user has no previous resources (e.g., models, concepts, etc.)that are applicable to document set 210 (step 330, No), the user maychoose to begin building a new model, for example by using N-gramsextracted from document set 210. For example, the user may define atleast one concept (step 350), and add the concept(s) to the model (step360), as described in more detail below with respect to FIGS. 12-33.

Next, the user may apply the concept(s) to document set 210 (step 370)to extract information, for example using the extraction processesdescribed above with respect to FIG. 3, and to review the results (step380), as described in more detail below with respect to FIG. 10. Theuser may at any point continue to manage concepts and revise the model,for example by adding or modifying concepts (step 390, Yes).

Step 320: Create Project

As described above, after downloading document set 210, a user maycreate a project using PIEM tool 205. FIG. 4 illustrates an exemplaryuser interface display of PIEM tool 205 consistent with an embodiment ofthe present invention for creating a new project. PIEM tool 205 maypresent menu 400 as shown in FIG. 4, which may provide the user withoptions related to the management and creation of projects and models.As shown in FIG. 4, menu 400 may present various options to the user,such as “Open Project” 401, “New Project” 402, “Export Project” 403,“Import Project” 404, “Delete Project” 405, “Close Project/Model” 406,and “Exit PIEM Tool” 407. Each menu option may also contain varioussub-options. For example, as shown in FIG. 4, menu option “New Project”402 contains sub-options “New Corpus and New Model” 410, “New Corpuswith Imported Model” 411, “Existing Corpus and New Model” 412, and“Existing Corpus with Imported Model” 413. One skilled in the art willrecognize that the menu options shown in FIG. 4 and in the other figuresin this application are merely for illustration, and that menu optionsmay be added to, deleted, or modified without departing the principlesof the invention.

Using PIEM tool 205 and menu 400, the user may create a new project, andan empty model 250 may be displayed. FIG. 5 illustrates an exemplaryuser interface display consistent with an embodiment of the presentinvention to display model 250. In the embodiment shown in FIG. 5, PIEMtool 205 may also display several default nodes representing concepts inmodel 250 (e.g., node “title” 501, node “publication date” 502, node“document notes” 503, node “status” 504, and node “concept” 505). A usermay also name its project. For example, in the embodiment shown in FIG.5, the user names the project “glu3.” In one embodiment, after creatinga new project, PIEM tool 205 may run an n-gram analysis on document set210, and process each document in document set 210 with a part-of-speechtagger, as described in more detail in the '847 application.

Steps 330-340: Import Concept into Project Using Available Resources

As described above with respect to FIG. 3, a user may begin to buildmodel 250 with existing resources. If the user has received a model, forexample from a colleague, the user may begin building model 250 usingresources (e.g., concepts and extractors) from the received model.Returning to FIG. 4, the user may select option New Project 402, andsub-option New Corpus with Imported Model 411. FIG. 6 illustrates anexemplary user interface display consistent with an embodiment of thepresent invention to import concepts into models. As shown in FIG. 6,PIEM tool 205 may use existing resources to display model 250 thatincludes nodes representing concepts of interest. These concepts mayinclude, for example, a textual or graphical representation ofinformation relevant to a user. In one embodiment, model 250 may includeone or more default concepts based on the results of raw text analysis.Alternatively or additionally, the user may build concepts. For example,the user may input the text to create a node representing a concept,such as concepts “patients hook” 601, “numberofPatientsWith” 602,“metastudy” 603, “to determine” 604, “aims” 605, “interventions” 606,“patientswith” 607, “conclusion” 608, and “study type” 609.

As an example, in a clinical trial abstract, one of the most importantkinds of information is a statement about the participants of the study.Researchers may communicate these characteristics in a formulaic way.For example, often researchers start a sentence with trigger phrasessuch as, “Patients with”, “Children admitted to hospital for”, and“Women suffering from”. Over time, users may accumulate a large set ofthese trigger phrases. Users may create another concept defined toinclude all sentences that contain trigger phrases related toparticipants of the study. With high reliability, a sentence with such aphrase may represent a highly enriched context in which to findinformation about clinical trial participants.

As another example, the statement of the “aims” of the clinical trialmay be defined in a concept. Such “aims” statements may have triggerphrases that start a sentence, such as, “The purpose of the study was”,“we aimed to determine”, “we sought to assess”, etc. Model 250, as shownin FIG. 6, has a node “aims” 605 representing a concept “aims”, whichmay include a list of trigger phrases related to the aims of a clinicaltrial. A user may define another concept (e.g., “treatment results”)based on the concept “aims” such that in a clinical trial abstract, inmore than 95% of the cases where a trigger phrase is found, theremainder of the sentence contains information about the goals of thatclinical trial. Using this definitional dependency, a model may beautomatically updated whenever the concept aims is modified. Forexample, if a user adds another trigger phrase to the concept “aims”,extraction information related to the concept “treatment results” may beautomatically updated. Alternatively or additionally, the user may benotified whenever a concept is updated or modified, and may be given theoption to update the model, concept, extraction information, or otherinformation based on a definitional dependency. Further, if a documentis added to document set 210, the model may update extractioninformation based only on the additional document, without the need tore-extract information for the entire document set. One skilled in theart will recognize that using triggers to locate specific,information-rich contexts is not restricted to medical documents, asmany different kinds of texts may contain information that is introducedor associated with some kind of trigger phrase.

FIG. 7 is an exemplary user interface display consistent with anembodiment of the present invention that may define synonyms forconcepts. As shown in FIG. 7, a user may create synonyms for theconcepts in model 250 using synonym window 700. To add synonyms to aconcept, the user may select, e.g., right click, on the desired node inmodel 205, for example node “patients hook” 601, and tool 205 maydisplay Synonym Window 700. The user may add or delete words associatedwith each concept in model 250, as described in more detail in the '847application.

Step 370: Apply Concepts to Document Set

Each concept in model 250 may have an extractor assigned to it.Accordingly, if a user imports a concept, the user may also import itsassociated extractor. FIG. 8 is an exemplary user interface displayconsistent with an embodiment of the present invention that may extractinformation for concepts. As shown in FIG. 8, a user may navigate tomenu 800, which contains options “Refresh Pane” 801, “Corpus Analysis”802, and “Re-extract Concepts” 803, and may choose option “Re-extractConcepts” 803. PIEM tool 205 may then extract information from documentset 210 using the concepts in model 250, or may present extractionoptions, as described in more detail below with respect to FIG. 9.

FIG. 9 is an exemplary user interface display consistent with anembodiment of the present invention that may present extraction options.As shown in FIG. 9, after a user selects “Re-extract Concepts” 803, PIEMtool 205 may display Concept Chooser 900, and the user may then selectvarious concepts for extraction. Concepts may be listed in “Concept(Entity/Node)” column 901, and a checkbox or other selection means maybe listed in “Select” column 902. The user may select various conceptsfor extraction, or, in an one embodiment, PIEM tool 205 mayautomatically select concepts for extraction. A skilled artisan willappreciate that many other means and methods may be used to displayconcepts and methods of selection for purposes of extraction.

Step 380: Review Results

After selecting a concept for extraction, each node representing aconcept in model 250 may display the number of documents that containone or more occurrences of that concept. FIG. 10 illustrates anexemplary user interface display consistent with an embodiment of thepresent invention that displays the number of documents that containeach concept. For example, as shown in FIG. 10, node “patients hook” 601displays the number of documents 1010 (i.e., 673 documents) that containone or more occurrences of concept “patient hook” 601.

A user may also review other extraction results for a concept, forexample by selecting, e.g., clicking, on the node representing theconcept. FIG. 11 illustrates an exemplary user interface displayconsistent with an embodiment of the present invention that displaysextraction results. A user may clicked on node “patients with” 607, forexample, and PIEM tool 205 may display a results table 1110 withextracted information. As shown in FIG. 11, results table 1110 maycontain a document identification (e.g., a number), a trigger phrase orsynonym, and an excerpt of a document containing the trigger phrase orsynonym. As one skilled in the art will recognize, in this example theextraction process does not require reliance on the specific topic ofthe clinical trial abstracts, but instead may use commonly acceptedpatterns of speech in the selected category of documents. Once aspecific context is identified, the user may drill down into morespecific aspects of the clinical trials.

Steps 350-360: Define and Add Concepts

As an alternative, if a user does not have a model to work from, or ifthe user wishes to add concepts to an existing model, the user may startto define concepts that are meaningful for a specific document set. Auser may define concepts and add the concepts to the model, for exampleas described in the '847 application. FIG. 12 illustrates an exemplaryuser interface display consistent with an embodiment of the presentinvention to add and define concepts. As an example, a user may defineconcepts by adding nodes “Type 1” 1210 and “Type 2” 1220, and may definesynonyms for those concepts, for example to include roman numerals I andII, respectively. The user may then extract those concepts and view theresults in results table 1110 and model 250. As shown in FIG. 12, thenumber of documents containing each concept is displayed in each noderepresenting that concept (i.e., node “Type 1” 1210 displays 79documents, and node “Type 2” 1220 displays 461 documents).

After defining and adding concepts to model 250, PIEM tool 205 maydisplay extraction results for the additional concepts. FIG. 13illustrates an exemplary user interface display consistent with anembodiment of the present invention that displays extraction results.The user may select, e.g., click on node 605 “aims” and select a “TableDrilldown” option to display “Table Drilldown” window 1300. The user mayuse “Table Drilldown” window 1300 to search extraction results inresults table 1110. Results table 1110 may contain any number ofresults, such as document identifications (e.g., numbers), triggerphrases, synonyms, concepts, document excerpts, etc.

Step 390: Concept Management

A user may refine and manage the concepts in a model by any number ofways. FIG. 14 illustrates an exemplary user interface display consistentwith an embodiment of the present invention that allows for conceptmanagement. If the model already has concepts that the user wants to usein a “drilldown” mode, the user may open an Advanced Concept Managerwindow 1400. Hierarchy panel 1410 displays a containment hierarchy thatgives the user an overview of which concepts are contained within otherconcepts. The top level of the containment hierarchy is a generalcontext 1420, which represents the most general context in which toextract or to view the results of extraction for document set 210. Inthe embodiment show in FIG. 14, the most general context to view resultsis the entire document in document set 210. One skilled in the art willrecognize that the most general context in which to view results maydepend on the type of information in document set 210. The next level“tx” 1430 may include a single block of text. After the “whole document”general context 1420 and “tx” context 1430, panel 1410 may displaycontexts that result from the extraction of concepts. Panel 1440displays a list from which the user may select one or more concepts andcombinations thereof for additional searching. As shown in panel 1440,the user may search for concepts in a specified proximity to each other,as well as the order of concepts within document set 210.

FIG. 15 illustrates another exemplary user interface display consistentwith an embodiment of the present invention that allows for conceptmanagement. In this example, the user selects node 605 “Aims”, and inconcept selection panel 1440, selects only the concept “Type 1”. PIEMtool 205 calculates the subset of all instances of “Type 1” that appearwithin the “aims” context. FIG. 16 illustrates an exemplary userinterface display consistent with an embodiment of the present inventionthat displays results of concept management. As shown in FIG. 16,results table 1110 displays a table of all instances of “Type 1” thatappear within the “aims” context. For example, each row indicates adocument identification and a concept (i.e., “type 1”) found in thatdocument.

The user may click on a table row within results table 1110 to view adocument or excerpt. FIG. 17 illustrates an exemplary user interfacedisplay consistent with an embodiment of the present invention thatdisplays a document. As shown in FIG. 17, a user has selected table row1610 from results window 1110. PIEM tool 205 displays document window1700, which includes the selected document and highlighted segments 1710of the “Aims” concept.

FIG. 18 illustrates an exemplary user interface display consistent withan embodiment of the present invention that displays results of conceptmanagement. As shown in FIG. 18, a user may manipulate results table1110, for example by adding a column to results table 1110. Asillustrated in this example, the user may add a column to results table1110 to determine all instances of the concept “interventions” that arein the documents that contain the “Type 1” concept within the “aims”concept. One skilled in the art will recognize that the embodiment shownin FIG. 18 is just one example of a method to display results in PIEMtool 205, as many other methods of displaying results is possible.

FIG. 19 illustrates an exemplary user interface display consistent withan embodiment of the present invention that displays additions ofconcepts to a model. As shown in FIG. 19, the user may add concepts tomodel 250 at any time. As shown in this example, the user may add nodes1901-1910 that represent concepts related to treatments. In oneembodiment, PIEM tool 205 may store the date and time for events such asinitial document preprocessing, extraction of a specific concept,removal of a specific concept, modification of the definition of aspecific concept, or addition of a concept to model 250. Because PIEMtool 205 may store an extractor for each concept, changes to one conceptmay trigger a cascade of modifications depending on dependencies betweenconcept definitions, and the date or time at which each critical eventwas most recently executed. PIEM tool 205 may calculate any dependenciesbetween concept definitions, and may automatically update both model 250and extracted information (e.g., results table 1110 and document window1700) based on the calculation.

FIG. 20 illustrates an exemplary user interface display consistent withan embodiment of the present invention that displays relations betweenconcepts. As shown in FIG. 20, a user may select, e.g., mouse over, acertain node representing a concept, such as node 1901 “abarcose”, andmodel 250 may display any concepts that are collocated with the selectedconcept in collocation view 2000. In this example, each node isconnected to every other node in model 250, along with a representationof the number of documents that contain both nodes. For example, asshown in FIG. 20, representation 2010 indicates that only one documentincludes both of the concepts represented by nodes “acarbose” 1901 and“Type 1” 1220. FIG. 21 illustrates an exemplary user interface displayconsistent with an embodiment of the present invention that displaysrelations between concepts. As shown in FIG. 21, a user may determinewhich treatments occurred with “Type 1” concept 1220 by selecting node1220 and reviewing the results, for example in results table 1110.

FIG. 22 illustrates an exemplary user interface display consistent withan embodiment of the present invention for advanced concept management.As shown in FIG. 22, a user may return to the Advanced Concept Manager1400, select “aims” context 2200 in hierarchy panel 1410, and select the“type 1” concept using selection button 2210 to indicate that the userwants to search for the concept “type 1” within the results for theconcept “aims.”

FIG. 23 illustrates an exemplary user interface display consistent withan embodiment of the present invention for advanced concept management.A user may select menu “Table Actions” 2300 and select option “GenerateConcept” 2301 to generate a new concept containing the selections fromAdvanced Concept Manager 1400. PIEM tool 205 may request that the userenter a name for the new concept, and may then add a node representingthe new concept to model 250. FIG. 24 illustrates an exemplary userinterface display consistent with an embodiment of the present inventionfor advanced concept management. As shown in model 250 in FIG. 24, theuser has created new node “Aims—type 1” 2400 representing the newconcept created by the user. This simple, intuitive action is anotherway in which the user can create concepts in model 250. A table is analternative way of viewing a concept. In this case, the user asked PIEMtool 205 to create a specific table, and then to add its correspondingconcept to the model. In this way, every action a user performs can becaptured and stored in PIEM tool 205's internal extraction language. Ifat any point the user determines that a table is important or usefulenough to be treated as a concept in its own right, PIEM tool 205 maycreate the corresponding concept. Once this concept is added to model250, it is fully available for use with any other concept. For example,if new documents were added to document set 210, the user could ask PIEMtool 205 to extract “Aims—type 1” in those new documents and PIEM tool205 would know the entire process needed to extract that derivedconcept.

FIG. 25 illustrates an exemplary user interface display consistent withan embodiment of the present invention for advanced concept management.As shown in FIG. 25, the user may view the new node 2400 “Aims—type 1”in collocation view 2000 and review what treatments were discussed inclinical trial abstracts that also discuss type 1 patients with theiraims.

FIG. 26 illustrates an exemplary user interface display consistent withan embodiment of the present invention for advanced concept management.As shown in FIG. 26, a user may use Advanced Concept Manager window 1400to locate any documents that contain only the singular and plural of theword “conclusion.” From these results, the user may begin to build atrigger concept. After extracting the results for the concept“conclusion,” the user may ask PIEM tool 205 to return all occurrencesof concept “conclusion” together with the single sentence that containsit. FIG. 27 illustrates an exemplary user interface display consistentwith an embodiment of the present invention for concept management. PIEMtool 205 displays the result of the user's search for “conclusion” inresults window 1110. The user may again view any individual documentfrom results table 1110 in document window 1700, for example byselecting a row from results table 1110.

A user may also compute subsets of various concepts in model 250. FIG.28 illustrates an exemplary user interface display consistent with anembodiment of the present invention for computing subsets of concepts.As shown in FIG. 28, after having looked at treatments, the user may usePIEM tool 205 to compute a subset of concepts, for example, to locate aspecific result for all trials that compared insulin NPH and glargine,or more specifically, to find the conclusion statements within selectedtrials. To this end, as shown in FIG. 28, the user may open AdvancedConcept Manager 1400 and select the context “interventions.” Within“interventions”, the user may check “nph insulin” and “glargine.” FIG.29 illustrates an exemplary user interface display consistent with anembodiment of the present invention for displaying results of computingsubsets of concepts. As shown in FIG. 29, PIEM tool 205 responds to theuser selections shown in FIG. 28 with results table 1110, which displaysthe identifiers for documents whose “intervention” context containedboth “nph insulin” and “glargine.” A user may continue to computesubsets, as shown in FIGS. 28-29, to determine any number of subsets orcombinations of concepts in model 250.

As described above with respect to FIG. 3, a table may represent amulti-context information resource. Users may manipulate tables withinPIEM tool 205 for advanced concept management. FIG. 30 illustrates anexemplary user interface display consistent with an embodiment of thepresent invention for advanced concept management using tables. The usermay add a column to results window 1110 (not shown) by utilizing columnmanager 3000, and selecting from the “Available Columns” 3010 to add tothe “Installed Columns” 3020. In this way, a user may combine multipleexisting concepts into one single new concept. FIG. 31 illustratesanother exemplary user interface display consistent with an embodimentof the present invention for advanced concept management using tables.As shown in FIG. 31, the new column created in FIG. 30 appears inresults table 1110. In one embodiment, a user may save results table1110 as a new concept for model 250. In another embodiment, PIEM tool205 may automatically generate a new concept for model 250 upon creationof the new column in results table 1110.

As the user creates and manages model 250, he or she may at any timeview documents from document set 210 using PIEM tool 205. FIGS. 32-33illustrate exemplary user interface displays consistent with embodimentsof the present invention that allow a user to review selected documentsindividually in document window 1700. As shown in FIGS. 32-33, a usermay select a specific document in results table 1110, and the document,or a relevant excerpt from the document, will appear in document window1700. Portions of the document in window 1700 may indicate where aselected concept appears in the document.

FIG. 34 illustrates an exemplary user interface display consistent withan embodiment of the present invention for exporting information fromPIEM tool 205. A user may export model 250 or any subset of informationfrom model 250 using PIEM tool 205. In the example shown in FIG. 34, theuser may select various rows of results table 1110, navigate to menu3400 “Selected Rows Action”, and select from menu options such as“Reduce to Raw Text” 3401, “Delete Selected Documents from Project”3402, “Unlink Selected Documents from Concept” 3403, “Create Note Report3404,” and “Export Table” 3405. The user may select option “ExportTable” 3405 to export selected rows of the table as a tab-separated fileto pass to a colleague, for example, or may select option “Reduce to RawText” 3401 to save the selected rows of the table to a raw text file ona local computer. Alternatively or additionally, the user may selectoptions from menu “Document Set Tasks” 3410 to export or save documentsets, or may select options from menu “Table Actions” 3420 to export orsave tables.

Other embodiments of the invention will be apparent to those skilled inthe art from consideration of the specification and practice of theinvention disclosed herein. It is intended that the specification andexamples be considered as exemplary only. For example, a public websitemay serve for the exchange of models, where people share, trade, buy, orsell models on the website. The website may collect not only models, butalso references to documents that a contributor used in developing amodel. An owner of the website would be in a position to reconstituteprojects using models and document references to build a mapping thatmaps document sets to models. This mapping could be used in a“match-making” service, such that if a person input a set of documentreferences, the website could suggest well-matched models. If a personinput a model, the site could suggest a well-matched set of documentreferences. Server-based versions of the technology make it easy forteams to share and work on the same projects. All of the algorithms forextraction and analysis may use a computing cluster, for example, tomanage extremely large data sets or to accelerate processing. Further,graphical representation of data (pie charts, graphs, histograms, etc.)is also possible using the PIEM tool. Using the PIEM tool to create amodel that becomes a step in a data pipeline (e.g., commit extracteddata to specific fields in a database) leverages the power of anyexisting database. The PIEM tool may also include a “create database”plug-in that may automatically create a database for a model, so thatthe user receives a database that is customized to the model.

1. A method for modeling information implemented using a computer havinga processor and a display from a set of documents, comprising: importinga set of concepts; creating a model including the concepts; based on auser selection of a first concept, extracting first information from theset of documents using an extractor corresponding to the first concept,the first information comprising a list of documents containing thefirst concept; based on the first information, defining a context of thefirst concept comprising a contiguous block of text in proximity of thefirst concept in each document in the list of documents containing thefirst concept; based on a user selection of a second concept, extractingsecond information from the set of documents, the second informationcomprising a list of documents containing the second concept in thedefined context of the first concept; adding a new additional concept tothe model wherein the new additional concept represents the secondconcept in the defined context of the first concept; and extractinginformation related to the new additional concept from the set ofdocuments using an extractor corresponding to the new additionalconcept.
 2. The method of claim 1, wherein the list of documentscontaining the first concept comprises a document identifier for each ofthe documents.
 3. The method of claim 1, wherein the extractedinformation related to the new additional concept comprises a list ofdocuments containing the second concept in the defined context of thefirst concept.
 4. The method of claim 1, wherein the first informationfurther comprises an excerpt from each of the documents containing thefirst concept.
 5. The method of claim 1, further comprising: based on auser selection of a third concept, extracting third information from theset of documents, the third information comprising a list of documentscontaining the third concept and the second concept in the definedcontext of the first concept.
 6. The method of claim 1, furthercomprising: automatically generating a database customized to the model.7. The method of claim 1, further comprising: selecting the set ofconcepts based on the set of documents.
 8. The method of claim 1,further comprising: determining a trigger phrase related to the set ofdocuments; and creating a second new additional concept based on thetrigger phrase.
 9. The method of claim 1, further comprising: exportingthe model including the new additional concept to another computer. 10.A method for personalizing a model of information implemented using acomputer having a processor and a display, comprising: obtaining a setof documents; receiving the model that contains concepts; extractingfirst information from the set of documents using an extractorcorresponding to a first concept, the first information comprising alist of documents containing the first concept; based on the firstinformation, defining a context of the first concept comprising acontiguous block of text in proximity of the first concept in eachdocument in the list of documents containing the first concept;selecting a second concept to update; updating the second concept;extracting second information from the set of documents, the secondinformation comprising a list of documents containing the updated secondconcept in the defined context of the first concept; adding a newadditional concept to the model wherein the new additional conceptrepresents the updated second concept in the defined context of thefirst concept; and extracting information related to the new additionalconcept from the set of documents using an extractor corresponding tothe new additional concept.
 11. The method of claim 10, wherein thedefined context of the first concept further comprises each document inthe list of documents containing the first concept.
 12. The method ofclaim 10, wherein the defined context of the first concept furthercomprises a subset of the documents containing the first concept. 13.The method of claim 10, wherein the defined context of the first conceptfurther comprises a section of a document in the list of documentscontaining the first concept.
 14. The method of claim 10, wherein thedefined context of the first concept further comprises a status of adocument in the list of documents containing the first concept.
 15. Themethod of claim 10, further comprising: automatically assigning anextractor to the new additional concept.
 16. The method of claim 10,further comprising: exporting the model including the new additionalconcept.
 17. A method for annotating a set of documents in a model ofinformation implemented using a computer having a processor and adisplay, comprising: downloading a set of documents; receiving themodel, wherein the model contains concepts; extracting first informationfrom the set of documents using an extractor corresponding to a firstconcept, the first information comprising a list of documents containingthe first concept; calculating a status of a document in the set ofdocuments; after extracting the first information, automaticallyannotating a document in the set of documents based on the calculation;based on the first information, defining a context of the first conceptcomprising a contiguous block of text in proximity of the first conceptin each document in the list of documents containing the first concept;extracting second information from the set of documents, the secondinformation comprising a list of documents containing a second conceptin the defined context of the first concept; adding a new additionalconcept to the model wherein the new additional concept represents thesecond concept in the defined context of the first concept; andextracting information related to the new additional concept from theset of documents using an extractor corresponding to the new additionalconcept.
 18. The method of claim 17, further comprising: displaying, onthe display device, the model using an entity-relationship diagram,wherein the concepts are depicted as entities and relationships betweenthe concepts are depicted as relations between entities.
 19. The methodof claim 17, wherein calculating is based on a function provided by auser.
 20. The method of claim 17, further comprising: receiving adefinition for the function from the user.
 21. A method for modelinginformation implemented using a computer having a processor and adisplay from a set of documents, comprising: importing a set of conceptsand corresponding extractors; creating a model including a first conceptand a second concept; establishing a definitional dependency between thefirst concept and the second concept; based on a user selection of thefirst concept, extracting first information from the set of documentsusing an extractor corresponding to the first concept, the firstinformation comprising a list of documents containing the first concept;based on the first information, defining a context of the first conceptcomprising a contiguous block of text in proximity of the first conceptin each document in the list of documents containing the first concept;after extracting information related to the first concept, receiving amodification of the second concept; after receiving the modification ofthe second concept, updating the first information using thedefinitional dependency between the first concept and the secondconcept; adding a new additional concept to the model wherein the newadditional concept represents the updated first information using thedefinitional dependency between the first concept and the secondconcept; and based on a user selection of the new additional concept,extracting information related to the new additional concept from theset of documents using an extractor corresponding to the new additionalconcept.
 22. The method of claim 21, further comprising: receiving anadditional document for the set of documents after extractinginformation related to the first concept; and updating the firstinformation based on the additional document.
 23. The method of claim21, further comprising: notifying a user of the modification of thesecond concept; and receiving a request from the user to update thefirst information.
 24. A system for modeling information from a set ofdocuments, comprising: a processor; an extraction engine configured inthe processor to extract information from the set of documents; softwarecomponents comprising: an importing component configured to import a setof concepts, a modeling component configured to create a model includingthe concepts, a first extraction component configured to cause theextraction engine to extract first information from the set of documentsusing an extractor corresponding to the first concept, the firstinformation comprising a list of documents containing a first concept, acontext component for, based on the first information, defining acontext of the first concept comprising a contiguous block of text inproximity of the first concept in each document in the list of documentscontaining the first concept, a second extraction component configuredto cause the extraction engine to extract second information from theset of documents, the second information comprising a list of documentscontaining a second concept in the defined context of the first concept,a context concept component configured to add a new additional conceptto the model wherein the new additional concept represents the secondconcept in the defined context of the first concept, and a contextextraction component configured to cause the extraction engine toextract information related to the new additional concept from the setof documents using an extractor corresponding to the new additionalconcept; and a database configured to store the model.